Altered DNA copy number is one of the many ways that gene expression and function may be modified. Some variations can be found among normal individuals, others occur in the course of normal processes in some species, and still others participate in causing various disease states. For example, many defects in human development are due to gains and losses of chromosomes and chromosomal segments that occur prior to or shortly after fertilization, whereas DNA dosage alterations that occur in somatic cells are frequent contributors to cancer. Therefore, detection of such aberrations, and interpreting them within the context of broader knowledge, facilitates identification of critical genes and pathways involved in biological processes and diseases, and provides clinically relevant information, such as in identifying efficacious drug regimes.
In normal diploid organisms, autosomal chromosomes are present in two identical copies, although polyploid cells have multiple copies of chromosomes and haploid cells have single copies. The chromosomes are arranged and displayed (often on a photo) in a standard format known as an idiogram: in pairs, ordered by size and position of centromere for chromosomes of the same size. Karyotypes are used to study chromosomal aberrations, and may be used to determine other macroscopically visible aspects of an individual's genotype, such as sex. In order to be able to see the chromosomes and determine their size and internal pattern, they are chemically labeled with a dye (“stained”). The resulting pattern of individual chromosomes is called chromosome banding. One of the most common staining methods is called “G-banding.” Other staining methods are available to help identify specific abnormalities.
Visualization of human chromosomes in somatic cells requires that dividing cells be studied during mitosis. Large numbers of metaphase cells can best be obtained by growing cells in culture and adding spindle poisons to cell cultures during periods of active growth to arrest cells in metaphase. While the number of cells found in metaphase will increase with increased exposure to the spindle poison, chromosome condensation also progresses with time. A key element in the preparation of analyzable chromosome spreads is the degree of dispersion of the chromosomes on the microscope slide. The ideal metaphase spread has all 46 chromosomes dispersed in the same optical field under the microscope, with no overlapping chromosomes. For clinical study, it is desirable to find at least 20-30 analyzable metaphase chromosome cells for each patient. Since not all cells are engaged in cell division, and not all cells are in the metaphase stage, the cytogenic technologist must frequently examine a large number of cells under multiple microscope objectives to find a sufficient number of analyzable cells, looking at as many as 5-10 slides. Once the analyzable cells are identified, the standard procedure is to photograph, or digitize onto computer media, the entire metaphase spread, cut out the individual chromosomes (actually or electronically), and arrange the chromosomes in a standard karyotype where both homologues of each chromosome pair placed side by side in numerical order. Frequently, the chromosomes in metaphase images are bent or curved so that, prior to separating and arranging the chromosome images for comparison, they must be reshaped into a generally straight line. In order to complete this step, the images must be further manipulated to allow side-by-side comparison. Thus, a great deal of time is required before even reaching the point at which evaluation of the sample for abnormalities can begin.
Once the images are properly arranged in this manner, band-by-band analysis can be performed, allowing identification of changes caused by structural chromosome abnormalities. The number of bands that are discernible in a single metaphase chromosome spread may vary from under 300 to approximately 1,400. Multiplied by 20 or 30, the entire process becomes an extremely labor-intensive, lengthy and inefficient process that can introduce critical delays in the treatment of patients as well as inconsistencies in diagnostic performance due to inter- and intra-reader variability. Accordingly, there is a need for a system and method to significantly speed up and improve the repeatability of the process of searching for and identifying analyzable chromosomes, and analyzing the chromosomes for abnormalities. An automated computer system capable of processing metaphase images, separating chromosomes, and detecting chromosome abnormalities would greatly enhance the usefulness, cost-effectiveness and availability of cytogenetic diagnostic testing. The present invention is directed to such a system and method.